123. Gil N, Fajardo EJ, Fiser A article icon
Discovery of receptor-ligand interfaces in the immunoglobulin superfamily.
(2020) 88(1) : 135-142
PMID: 31298437     PMCID:

122. Fajardo JE, Shrestha R, Gil N, Belsom A, Crivelli SN, Czaplewski C, Fidelis K, Grudinin S, Karasikov M, Karczynska AS, Kryshtafovych A, Leitner A, Liwo A, Lubecka EA, Monastyrskyy B, Pages G, Rappsilber J, Sieradzan AK, Sikorska C, Trabjerg E, Fiser A article icon
Assessment of chemical-crosslink-assisted protein structure modeling in CASP13.
(2019) 87(12) : 1283-1297
PMID: 31569265     PMCID: PMC6851497

121. Shrestha R, Fajardo E, Gil N, Fidelis K, Kryshtafovych A, Monastyrskyy B, Fiser A article icon
Assessing the accuracy of contact predictions in CASP13.
(2019) 87(12) : 1058-1068
PMID: 31587357     PMCID: PMC6851495

120. Viswanathan R, Fajardo E, Steinberg G, Haller M, Fiser A article icon
Protein-protein binding supersites.
PLoS Comput Biol
(2019) 15(1) : e1006704
PMID: 30615604     PMCID: PMC6336348

119. Zepecki JP, Snyder KM, Moreno MM, Fajardo E, Fiser A, Ness J, Sarkar A, Toms SA, Tapinos N article icon
Regulation of human glioma cell migration, tumor growth, and stemness gene expression using a Lck targeted inhibitor.
(2019) 38(10) : 1734-1750
PMID: 30353164     PMCID: PMC6462869

118. Aluri S, Zhao R, Lin K, Shin DS, Fiser A, Goldman ID article icon
Substitutions that lock and unlock the proton-coupled folate transporter (PCFT-SLC46A1) in an inward-open conformation.
J Biol Chem
(2019) 294(18) : 7245-7258
PMID: 30858177     PMCID: PMC6509503

117. Shrestha R, Garrett SC, Almo SC, Fiser A article icon
Computational Redesign of PD-1 Interface for PD-L1 Ligand Selectivity.
(2019) 27(5) : 829-836.e3
PMID: 30930066     PMCID: PMC6745709

116. Ajasin DO, Rao VR, Wu X, Ramasamy S, Pujato M, Ruiz AP, Fiser A, Bresnick AR, Kalpana GV, Prasad VR article icon
CCL2 mobilizes ALIX to facilitate Gag-p6 mediated HIV-1 virion release.
(2019) 8,
PMID: 31172941     PMCID: PMC6592687

115. Aluri S, Zhao R, Fiser A, Goldman ID article icon
Substituted-cysteine accessibility and cross-linking identify an exofacial cleft in the 7th and 8th helices of the proton-coupled folate transporter (SLC46A1).
Am J Physiol Cell Physiol
(2018) 314(3) : C289-C296
PMID: 29167151     PMCID:

114. Aluri S, AUID- ORCID: 0000-0003-4084-1747, Zhao R, Lubout C, Goorden SMI, Fiser A, Goldman ID article icon
Hereditary folate malabsorption due to a mutation in the external gate of the proton-coupled folate transporter SLC46A1.
Blood Adv
(2018) 2(1) : 61-68
PMID: 29344585     PMCID: PMC5761628

113. Ducati RG, Namanja-Magliano HA, Harijan RK, Fajardo JE, Fiser A, Daily JP, Schramm VL article icon
Genetic resistance to purine nucleoside phosphorylase inhibition in Plasmodium falciparum.
Proc Natl Acad Sci U S A
(2018) 115(9) : 2114-2119
PMID: 29440412     PMCID:

112. Gil N, Fiser A article icon
The choice of sequence homologs included in multiple sequence alignments has a dramatic impact on evolutionary conservation analysis.
(2018) ,
PMID: 29947739     PMCID:

111. Gil N, Fiser A article icon
Identifying Functionally Informative Evolutionary Sequence Profiles.
(2017) ,
PMID: 29211823     PMCID:

110. Aluri S, Zhao R, Fiser A, Goldman ID article icon
Residues in the eighth transmembrane domain of the proton-coupled folate transporter (SLC46A1) play an important role in defining the aqueous translocation pathway and in folate substrate binding.
Biochim Biophys Acta
(2017) 1859(11) : 2193-2202
PMID: 28802835     PMCID: PMC5624325

109. Carvallo L, Lopez L, Fajardo JE, AUID- ORCID: http://orcid.org/0000-0001-9701-8546, Jaureguiberry-Bravo M, Fiser A, Berman JW article icon
HIV-Tat regulates macrophage gene expression in the context of neuroAIDS.
PLoS One
(2017) 12(6) : e0179882
PMID: 28640909     PMCID: PMC5481010

108. Najmi M, Zhao R, Fiser A, Goldman ID article icon
Role of the tryptophan residues in proton-coupled folate transporter (PCFT-SLC46A1) function.
Am J Physiol Cell Physiol
(2016) 311(1) : C150-7
PMID: 27251438     PMCID:

107. Ness JK, Skiles AA, Yap EH, Fajardo EJ, Fiser A, Tapinos N article icon
Nuc-ErbB3 regulates H3K27me3 levels and HMT activity to establish epigenetic repression during peripheral myelination.
(2016) 64(6) : 977-92
PMID: 27017927     PMCID:

106. Zhao R, Najmi M, Fiser A, Goldman ID article icon
Identification of an Extracellular Gate for the Proton-coupled Folate Transporter (PCFT-SLC46A1) by Cysteine Cross-linking.
J Biol Chem
(2016) 291(15) : 8162-72
PMID: 26884338     PMCID: PMC4825018

105. Yang CH, Yap EH, Xiao H, Fiser A, Horwitz SB article icon
2-(m-Azidobenzoyl)taxol binds differentially to distinct beta-tubulin isotypes.
Proc Natl Acad Sci U S A
(2016) 113(40) : 11294-11299
PMID: 27651486     PMCID: PMC5056068

104. Dybas JM, Fiser A article icon
Development of a motif-based topology-independent structure comparison method to identify evolutionarily related folds.
(2016) 84(12) : 1859-1874
PMID: 27671894     PMCID: PMC5118133

103. Cao LL, Riascos-Bernal DF, Chinnasamy P, Dunaway CM, Hou R, Pujato MA, O'Rourke BP, Miskolci V, Guo L, Hodgson L, Fiser A, Sibinga NE article icon
Control of mitochondrial function and cell growth by the atypical cadherin Fat1.
(2016) 539(7630) : 575-578
PMID: 27828948     PMCID: PMC5257202

102. Yap EH, Fiser A article icon
ProtLID, a Residue-Based Pharmacophore Approach to Identify Cognate Protein Ligands in the Immunoglobulin Superfamily.
(2016) 24(12) : 2217-2226
PMID: 27889206     PMCID:

101. Vallat B, Madrid-Aliste C, Fiser A article icon
Modularity of Protein Folds as a Tool for Template-Free Modeling of Structures.
PLoS Comput Biol
(2015) 11(8) : e1004419
PMID: 26252221     PMCID: PMC4529212

100. Carvallo L, Lopez L, Che FY, Lim J, Eugenin EA, Williams DW, Nieves E, Calderon TM, Madrid-Aliste C, Fiser A, Weiss L, Angeletti RH, Berman JW article icon
Buprenorphine decreases the CCL2-mediated chemotactic response of monocytes.
J Immunol
(2015) 194(7) : 3246-58
PMID: 25716997     PMCID: PMC4369415

99. Janakiram M, Chinai JM, Fineberg S, Fiser A, Montagna C, Medavarapu R, Castano E, Jeon H, Ohaegbulam KC, Zhao R, Zhao A, Almo SC, Sparano JA, Zang X article icon
Expression, Clinical Significance, and Receptor Identification of the Newest B7 Family Member HHLA2 Protein.
Clin Cancer Res
(2015) 21(10) : 2359-66
PMID: 25549724     PMCID: PMC4433806

98. Visentin M, Unal ES, Najmi M, Fiser A, Zhao R, Goldman ID article icon
Identification of Tyr residues that enhance folate substrate binding and constrain oscillation of the proton-coupled folate transporter (PCFT-SLC46A1).
Am J Physiol Cell Physiol
(2015) 308(8) : C631-41
PMID: 25608532     PMCID: PMC4398847

97. Yap EH, Rosche T, Almo S, Fiser A article icon
Functional clustering of immunoglobulin superfamily proteins with protein-protein interaction information calibrated hidden markov model sequence profiles.
J Mol Biol
(2014) 426(4) : 945-61
PMID: 24246499     PMCID:

96. Xie Q, Ung D, Khafizov K, Fiser A, Cvekl A article icon
Gene regulation by PAX6: structural-functional correlations of missense mutants and transcriptional control of Trpm3/miR-204.
Mol Vis
(2014) 20, 270-82
PMID: 24623969     PMCID: PMC3945805

95. Khafizov K, Madrid-Aliste C, Almo SC, Fiser A article icon
Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative.
Proc Natl Acad Sci U S A
(2014) 111(10) : 3733-8
PMID: 24567391     PMCID: PMC3956173

94. Tudos E, Meszaros B, Fiser A, Simon I article icon
A word of caution about biological inference - Revisiting cysteine covalent state predictions.
FEBS Open Bio
(2014) 4, 310-4
PMID: 24918043     PMCID: PMC4048844

93. Pujato M, Kieken F, Skiles AA, Tapinos N, Fiser A article icon
Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes.
Nucleic Acids Res
(2014) 42(22) : 13500-12
PMID: 25428367     PMCID: PMC4267649

92. Fernandez-Fuentes N, Fiser A article icon
A modular perspective of protein structures: application to fragment based loop modeling.
Methods Mol Biol
(2013) 932, 141-58
PMID: 22987351     PMCID: PMC3635063

91. Pujato M, MacCarthy T, Fiser A, Bergman A article icon
The underlying molecular and network level mechanisms in the evolution of robustness in gene regulatory networks.
PLoS Comput Biol
(2013) 9(1) : e1002865
PMID: 23300434     PMCID: PMC3536627

90. Fajardo JE, Fiser A article icon
Protein structure based prediction of catalytic residues.
BMC Bioinformatics
(2013) 14, 63
PMID: 23433045     PMCID: PMC3598644

89. Soniat M, Sampathkumar P, Collett G, Gizzi AS, Banu RN, Bhosle RC, Chamala S, Chowdhury S, Fiser A, Glenn AS, Hammonds J, Hillerich B, Khafizov K, Love JD, Matikainen B, Seidel RD, Toro R, Rajesh Kumar P, Bonanno JB, Chook YM, Almo SC article icon
Crystal structure of human Karyopherin beta2 bound to the PY-NLS of Saccharomyces cerevisiae Nab2.
J Struct Funct Genomics
(2013) 14(2) : 31-5
PMID: 23535894     PMCID: PMC3681870

88. Shin DS, Zhao R, Fiser A, Goldman ID article icon
Role of the fourth transmembrane domain in proton-coupled folate transporter function as assessed by the substituted cysteine accessibility method.
Am J Physiol Cell Physiol
(2013) 304(12) : C1159-67
PMID: 23552283     PMCID: PMC3680650

87. Rubinstein R, Ramagopal UA, Nathenson SG, Almo SC, Fiser A article icon
Functional classification of immune regulatory proteins.
(2013) 21(5) : 766-76
PMID: 23583034     PMCID: PMC3654037

86. Menon V, Vallat BK, Dybas JM, Fiser A article icon
Modeling proteins using a super-secondary structure library and NMR chemical shift information.
(2013) 21(6) : 891-9
PMID: 23685209     PMCID: PMC3703203

85. Shin DS, Zhao R, Yap EH, Fiser A, Goldman ID article icon
A P425R mutation of the proton-coupled folate transporter causing hereditary folate malabsorption produces a highly selective alteration in folate binding.
Am J Physiol Cell Physiol
(2012) ,
PMID: 22345511     PMCID: PMC3361945

84. Lakshmanan V, Rhee K, Wang W, Yu Y, Khafizov K, Fiser A, Wu P, Ndir O, Mboup S, Ndiaye D, Daily J article icon
Metabolomic analysis of patient plasma yields evidence of plant-like alpha-linolenic acid metabolism in Plasmodium falciparum.
J Infect Dis
(2012) ,
PMID: 22566569     PMCID: PMC3490690

83. Zhao R, Shin DS, Fiser A, Goldman ID article icon
Identification of a functionally critical GXXG motif and its relationship to the folate binding site of the proton-coupled folate transporter (PCFT-SLC46A1).
Am J Physiol Cell Physiol
(2012) 303(6) : C673-81
PMID: 22785121     PMCID: PMC3468349

82. Shin DS, Zhao R, Fiser A, Goldman DI article icon
Functional roles of the A335 and G338 residues of the proton-coupled folate transporter (PCFT-SLC46A1) mutated in hereditary folate malabsorption.
Am J Physiol Cell Physiol
(2012) 303(8) : C834-42
PMID: 22843796     PMCID: PMC3469714

81. Che FY, Madrid-Aliste C, Burd B, Zhang H, Nieves E, Kim K, Fiser A, Angeletti RH, Weiss LM article icon
Comprehensive proteomic analysis of membrane proteins in Toxoplasma gondii.
Mol Cell Proteomics
(2011) 10(1) : M110.000745
PMID: 20935347     PMCID: PMC3013445

80. Khrapunovich-Baine M, Menon V, Huang Yang CP, Northcote PT, Miller JH, Hogue Angeletti R, Fiser A, Horwitz SB, Xiao H article icon
Hallmarks of molecular action of microtubule stabilizing agents: Effects of epothilone B, ixabepilone, peloruside A, and laulimalide on microtubule conformation.
J Biol Chem
(2011) ,
PMID: 21245138     PMCID: PMC3064228

79. Adilakshmi T, Ness-Myers J, Madrid-Aliste C, Fiser A, Tapinos N article icon
A Nuclear Variant of ErbB3 Receptor Tyrosine Kinase Regulates Ezrin Distribution and Schwann Cell Myelination.
J Neurosci
(2011) 31(13) : 5106-19
PMID: 21451047     PMCID: PMC3086203

78. Wang L, Rubinstein R, Lines JL, Wasiuk A, Ahonen C, Guo Y, Lu LF, Gondek D, Wang Y, Fava RA, Fiser A, Almo S, Noelle RJ article icon
VISTA, a novel mouse Ig superfamily ligand that negatively regulates T cell responses.
J Exp Med
(2011) 208(3) : 577-92
PMID: 21383057     PMCID: PMC3058578

77. Lim J, Menon V, Bitzer M, Miller LM, Madrid-Aliste C, Weiss LM, Fiser A, Angeletti RH article icon
Frozen tissue can provide reproducible proteomic results of subcellular fractionation.
Anal Biochem
(2011) ,
PMID: 21802400     PMCID: PMC3164751

76. Yan F, Che FY, Nieves E, Weiss LM, Angeletti RH, Fiser A article icon
Photo-assisted peptide enrichment in protein complex cross-linking analysis of a model homodimeric protein using mass spectrometry.
(2011) 11(20) : 4109-15
PMID: 21834138     PMCID: PMC3465073

75. Xiao H, El Bissati K, Verdier-Pinard P, Burd B, Zhang H, Kim K, Fiser A, Angeletti RH, Weiss LM article icon
Post-translational modifications to Toxoplasma gondii alpha- and beta-tubulins include novel C-terminal methylation.
J Proteome Res
(2010) 9(1) : 359-72
PMID: 19886702     PMCID: PMC2813730

74. Rykunov D, Fiser A article icon
New statistical potential for quality assessment of protein models and a survey of energy functions.
BMC Bioinformatics
(2010) 11, 128
PMID: 20226048     PMCID: PMC2853469

73. Fernandez-Fuentes N, Dybas JM, Fiser A article icon
Structural characteristics of novel protein folds.
PLoS Comput Biol
(2010) 6(4) : e1000750
PMID: 20421995     PMCID: PMC2858679

72. Sampathkumar P, Lu F, Zhao X, Li Z, Gilmore J, Bain K, Rutter ME, Gheyi T, Schwinn KD, Bonanno JB, Pieper U, Fajardo JE, Fiser A, Almo SC, Swaminathan S, Chance MR, Baker D, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Sali A, Sauder JM, Burley SK article icon
Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution.
(2010) 78(14) : 3056-62
PMID: 20737437     PMCID: PMC2989796

71. Shin DS, Min SH, Russell L, Zhao R, Fiser A, Goldman ID article icon
Functional roles of aspartate residues of the human proton-coupled folate transporter (PCFT; SLC46A1); D156, mutated in hereditary folate malabsorption, is critical for protein stability; D109 is irreplaceable.
(2010) ,
PMID: 20805364     PMCID: PMC3012536

70. Fiser A article icon
Template-based protein structure modeling.
Methods Mol Biol
(2010) 673, 73-94
PMID: 20835794     PMCID:

69. Dbouk HA, Pang H, Fiser A, Backer JM article icon
A biochemical mechanism for the oncogenic potential of the p110beta catalytic subunit of phosphoinositide 3-kinase.
Proc Natl Acad Sci U S A
(2010) 107(46) : 19897-902
PMID: 21030680     PMCID: PMC2993364

68. Rykunov D, Steinberger E, Madrid-Aliste CJ, Fiser A article icon
Improved scoring function for comparative modeling using the M4T method.
J Struct Funct Genomics
(2009) 10(1) : 95-9
PMID: 18985440     PMCID:

67. Madrid-Aliste CJ, Dybas JM, Hogue Angeletti R, Weiss LM, Kim K, Simon I, Fiser A article icon
EPIC-DB: a proteomics database for studying Apicomplexan organisms.
BMC Genomics
(2009) 10(1) : 38
PMID: 19159464     PMCID: PMC2652494

66. Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL Jr, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR Jr, Kortemme T, Kryshtafovych A, Montelione GT, article icon
Outcome of a workshop on applications of protein models in biomedical research.
(2009) 17(2) : 151-9
PMID: 19217386     PMCID: PMC2739730

65. Nair R, Liu J, Soong TT, Acton TB, Everett JK, Kouranov A, Fiser A, Godzik A, Jaroszewski L, Orengo C, Montelione GT, Rost B article icon
Structural genomics is the largest contributor of novel structural leverage.
J Struct Funct Genomics
(2009) 10(2) : 181-91
PMID: 19194785     PMCID: PMC2705706

64. Blakaj DM, Fernandez-Fuentes N, Chen Z, Hegde R, Fiser A, Burk RD, Brenowitz M article icon
Evolutionary and biophysical relationships among the papillomavirus E2 proteins.
Front Biosci
(2009) 14, 900-17
PMID: 19273107     PMCID: PMC3705561

63. Unal ES, Zhao R, Chang MH, Fiser A, Romero MF, Goldman ID article icon
The functional roles of the His247 and His281 residues in folate and proton translocation mediated by the human proton-coupled folate transporter (PCFT-SLC46A1).
J Biol Chem
(2009) 284(26) : 17846-57
PMID: 19389703     PMCID: PMC2719423

62. Weiss LM, Fiser A, Angeletti RH, Kim K article icon
Toxoplasma gondii proteomics.
Expert Rev Proteomics
(2009) 6(3) : 303-13
PMID: 19489701     PMCID: PMC2741161

61. Dessailly BH, Nair R, Jaroszewski L, Fajardo JE, Kouranov A, Lee D, Fiser A, Godzik A, Rost B, Orengo C article icon
PSI-2: Structural Genomics to Cover Protein Domain Family Space.
(2009) 17(6) : 869-81
PMID: 19523904     PMCID: PMC2920419

60. Abboud N, De Jesus M, Nakouzi A, Cordero RJ, Pujato M, Fiser A, Rivera J, Casadevall A article icon
Identification of linear epitopes in bacillus anthracis protective antigen bound by neutralizing antibodies.
J Biol Chem
(2009) 284(37) : 25077-86
PMID: 19617628     PMCID: PMC2757211

59. Yan F, Che FY, Rykunov D, Nieves E, Fiser A, Weiss LM, Hogue Angeletti R article icon
Nonprotein Based Enrichment Method to Analyze Peptide Cross-Linking in Protein Complexes.
Anal Chem
(2009) 81(17) : 7149-59
PMID: 19642656     PMCID: PMC2765915

58. Grozdanov PN, Fernandez-Fuentes N, Fiser A, Meier UT article icon
Pathogenic NAP57 mutations decrease ribonucleoprotein assembly in dyskeratosis congenita.
Hum Mol Genet
(2009) 18(23) : 4546-51
PMID: 19734544     PMCID: PMC2773269

57. Trofa D, Agovino M, Stehr F, Schafer W, Rykunov D, Fiser A, Hamari Z, Nosanchuk JD, Gacser A article icon
Acetylsalicylic acid (aspirin) reduces damage to reconstituted human tissues infected with Candida species by inhibiting extracellular fungal lipases.
Microbes Infect
(2009) 11(14-15) : 1131-9
PMID: 19703582     PMCID: PMC2787780

56. Khrapunovich-Baine M, Menon V, Verdier-Pinard P, Smith AB 3rd, Angeletti RH, Fiser A, Horwitz SB, Xiao H article icon
Distinct pose of discodermolide in taxol binding pocket drives a complementary mode of microtubule stabilization.
(2009) 48(49) : 11664-77
PMID: 19863156     PMCID: PMC2845443

55. Graslund S, Nordlund P, Weigelt J, Bray J, Gileadi O, Knapp S, Oppermann U, Arrowsmith C, Hui R, Ming J, dhe-Paganon S, Park HW, Savchenko A, Yee A, Edwards A, Vincentelli R, Cambillau C, Kim R, Kim SH, Rao Z, Shi Y, Terwilliger TC, Kim CY, Hung LW, Waldo article icon
Protein production and purification.
Nat Methods
(2008) 5(2) : 135-46
PMID: 18235434     PMCID: PMC3178102

54. Rubinstein R, Fiser A article icon
Predicting disulfide bond connectivity in proteins by correlated mutations analysis.
(2008) 24(4) : 498-504
PMID: 18203772     PMCID:

53. Dybas JM, Madrid-Aliste CJ, Che FY, Nieves E, Rykunov D, Angeletti RH, Weiss LM, Kim K, Fiser A article icon
Computational Analysis and Experimental Validation of Gene Predictions in Toxoplasma gondii.
(2008) 3(12) : e3899
PMID: 19065262     PMCID: PMC2587701

52. Torres M, Fernandez-Fuentes N, Fiser A, Casadevall A article icon
Exchanging murine and human immunoglobulin constant chains affects the kinetics and thermodynamics of antigen binding and chimeric antibody autoreactivity.
(2007) 2(12) : e1310
PMID: 18074033     PMCID: PMC2110899

51. Almo SC, Bonanno JB, Sauder JM, Emtage S, Dilorenzo TP, Malashkevich V, Wasserman SR, Swaminathan S, Eswaramoorthy S, Agarwal R, Kumaran D, Madegowda M, Ragumani S, Patskovsky Y, Alvarado J, Ramagopal UA, Faber-Barata J, Chance MR, Sali A, Fiser A, Zhang article icon
Structural genomics of protein phosphatases.
J Struct Funct Genomics
(2007) 8(2-3) : 121-40
PMID: 18058037     PMCID:

50. Fernandez-Fuentes N, Rai BK, Madrid-Aliste CJ, Fajardo JE, Fiser A article icon
Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments.
(2007) 23(19) : 2558-65
PMID: 17823132     PMCID:

49. Feyfant E, Sali A, Fiser A article icon
Modeling mutations in protein structures.
Protein Sci
(2007) 16(9) : 2030-41
PMID: 17766392     PMCID: PMC2206969

48. Fernandez-Fuentes N, Madrid-Aliste CJ, Rai BK, Fajardo JE, Fiser A article icon
M4T: a comparative protein structure modeling server.
Nucleic Acids Res
(2007) 35(Web S) : W363-8
PMID: 17517764     PMCID: PMC1933164

47. Torres M, Fernandez-Fuentes N, Fiser A, Casadevall A article icon
The immunoglobulin heavy chain constant region affects kinetic and thermodynamic parameters of antibody variable region interactions with antigen.
J Biol Chem
(2007) 282(18) : 13917-27
PMID: 17353196     PMCID:

46. Rykunov D, Fiser A article icon
Effects of amino acid composition, finite size of proteins, and sparse statistics on distance-dependent statistical pair potentials.
(2007) 67(3) : 559-68
PMID: 17335003     PMCID:

45. Manjasetty BA, Shi W, Zhan C, Fiser A, Chance MR article icon
A high-throughput approach to protein structure analysis.
Genet Eng (N Y)
(2007) 28, 105-28
PMID: 17153936     PMCID:

44. Vetting MW, Hegde SS, Fajardo JE, Fiser A, Roderick SL, Takiff HE, Blanchard JS article icon
Pentapeptide repeat proteins.
(2006) 45(1) : 1-10
PMID: 16388575     PMCID: PMC2566302

43. Rai BK, Fiser A article icon
Multiple mapping method: a novel approach to the sequence-to-structure alignment problem in comparative protein structure modeling.
(2006) 63(3) : 644-61
PMID: 16437570     PMCID:

42. Fernandez-Fuentes N, Oliva B, Fiser A article icon
A supersecondary structure library and search algorithm for modeling loops in protein structures.
Nucleic Acids Res
(2006) 34(7) : 2085-97
PMID: 16617149     PMCID: PMC1440879

41. Xiao H, Verdier-Pinard P, Fernandez-Fuentes N, Burd B, Angeletti R, Fiser A, Horwitz SB, Orr GA article icon
Insights into the mechanism of microtubule stabilization by Taxol.
Proc Natl Acad Sci U S A
(2006) 103(27) : 10166-73
PMID: 16801540     PMCID: PMC1502429

40. Fernandez-Fuentes N, Fiser A article icon
Saturating representation of loop conformational fragments in structure databanks.
BMC Struct Biol
(2006) 6, 15
PMID: 16820050     PMCID: PMC1574324

39. Fernandez-Fuentes N, Zhai J, Fiser A article icon
ArchPRED: a template based loop structure prediction server.
Nucleic Acids Res
(2006) 34(Web S) : W173-6
PMID: 16844985     PMCID: PMC1538831

38. Rai BK, Madrid-Aliste CJ, Fajardo JE, Fiser A article icon
MMM: a sequence-to-structure alignment protocol.
(2006) 22(21) : 2691-2
PMID: 16928737     PMCID:

37. Chattopadhyay K, Bhatia S, Fiser A, Almo SC, Nathenson SG article icon
Structural basis of inducible costimulator ligand costimulatory function: determination of the cell surface oligomeric state and functional mapping of the receptor binding site of the protein.
J Immunol
(2006) 177(6) : 3920-9
PMID: 16951355     PMCID:

36. Reichman C, Singh K, Liu Y, Singh S, Li H, Fajardo JE, Fiser A, Birge RB article icon
Transactivation of Abl by the Crk II adapter protein requires a PNAY sequence in the Crk C-terminal SH3 domain.
(2005) 24(55) : 8187-99
PMID: 16158059     PMCID:

35. Bonanno JB, Almo SC, Bresnick A, Chance MR, Fiser A, Swaminathan S, Jiang J, Studier FW, Shapiro L, Lima CD, Gaasterland TM, Sali A, Bain K, Feil I, Gao X, Lorimer D, Ramos A, Sauder JM, Wasserman SR, Emtage S, D'Amico KL, Burley SK article icon
New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative.
J Struct Funct Genomics
(2005) 6(2-3) : 225-32
PMID: 16211523     PMCID:

34. Zhan C, Fedorov EV, Shi W, Ramagopal UA, Thirumuruhan R, Manjasetty BA, Almo SC, Fiser A, Chance MR, Fedorov AA article icon
The ybeY protein from Escherichia coli is a metalloprotein.
Acta Crystallogr Sect F Struct Biol Cryst Commun
(2005) 61(Pt 11) : 959-63
PMID: 16511207     PMCID: PMC1978141

33. Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A article icon
MODBASE, a database of annotated comparative protein structure models, and associated resources.
Nucleic Acids Res
(2004) 32(Datab) : D217-22
PMID: 14681398     PMCID: PMC308829

32. Tudos E, Fiser A, Simon A, Dosztanyi Z, Fuxreiter M, Magyar C, Simon I article icon
Noncovalent cross-links in context with other structural and functional elements of proteins.
J Chem Inf Comput Sci
(2004) 44(2) : 347-51
PMID: 15032510     PMCID:

31. Chance MR, Fiser A, Sali A, Pieper U, Eswar N, Xu G, Fajardo JE, Radhakannan T, Marinkovic N article icon
High-throughput computational and experimental techniques in structural genomics.
Genome Res
(2004) 14(10B) : 2145-54
PMID: 15489337     PMCID: PMC528931

30. Fiser A article icon
Protein structure modeling in the proteomics era.
Expert Rev Proteomics
(2004) 1(1) : 97-110
PMID: 15966803     PMCID:

29. Lee SA, Shen EL, Fiser A, Sali A, Guo S article icon
The zebrafish forkhead transcription factor Foxi1 specifies epibranchial placode-derived sensory neurons.
(2003) 130(12) : 2669-79
PMID: 12736211     PMCID:

28. Dosztanyi Z, Magyar C, Tusnady GE, Cserzo M, Fiser A, Simon I article icon
Servers for sequence-structure relationship analysis and prediction.
Nucleic Acids Res
(2003) 31(13) : 3359-63
PMID: 12824327     PMCID: PMC168995

27. Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B, Sali A article icon
Tools for comparative protein structure modeling and analysis.
Nucleic Acids Res
(2003) 31(13) : 3375-80
PMID: 12824331     PMCID: PMC168950

26. Hargitai J, Lewis H, Boros I, Racz T, Fiser A, Kurucz I, Benjamin I, Vigh L, Penzes Z, Csermely P, Latchman DS article icon
Bimoclomol, a heat shock protein co-inducer, acts by the prolonged activation of heat shock factor-1.
Biochem Biophys Res Commun
(2003) 307(3) : 689-95
PMID: 12893279     PMCID:

25. Fiser A, Sali A article icon
ModLoop: automated modeling of loops in protein structures.
(2003) 19(18) : 2500-1
PMID: 14668246     PMCID:

24. Fiser A, Sali A article icon
Modeller: generation and refinement of homology-based protein structure models.
Methods Enzymol
(2003) 374, 461-91
PMID: 14696385     PMCID:

23. Fiser, A. and Sali, A article icon
Comparative protein structure modeling
Protein Structure: Determination, Analysis, and Application for Drug discovery. Marcel Dekker, New York,
(2003) , pp 167-206
PMID: 0     PMCID:

22. Marti-Renom MA., Fiser A., Madhusudhan M.S., John B., Stuart A., Eswar N., Pieper U., Shen, M-Y. and Sali, A. article icon
Modeling protein structure from its sequence
Current Protocols in Bioinformatics John Wiley and Sons, Inc. V. 5
(2003) , pp. 5.1.1.-5.1.32
PMID: 0     PMCID:

21. Fiser A, Filipe SR, Tomasz A article icon
Cell wall branches, penicillin resistance and the secrets of the MurM protein.
Trends Microbiol
(2003) 11(12) : 547-53
PMID: 14659686     PMCID:

20. Fiser A, Simon I article icon
Predicting redox state of cysteines in proteins.
Methods Enzymol
(2002) 353, 10-21
PMID: 12078485     PMCID:

19. Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B, Sali A article icon
Reliability of assessment of protein structure prediction methods.
(2002) 10(3) : 435-40
PMID: 12005441     PMCID:

18. Fiser A, Feig M, Brooks CL 3rd, Sali A article icon
Evolution and physics in comparative protein structure modeling.
Acc Chem Res
(2002) 35(6) : 413-21
PMID: 12069626     PMCID:

17. Vernal J, Fiser A, Sali A, Muller M, Cazzulo JJ, Nowicki C article icon
Probing the specificity of a trypanosomal aromatic alpha-hydroxy acid dehydrogenase by site-directed mutagenesis.
Biochem Biophys Res Commun
(2002) 293(1) : 633-9
PMID: 12054650     PMCID:

16. A. Fiser, R. Sánchez, F. Melo and A. Sali. article icon
Comparative protein structure modeling in Computational Biochemistry and Biophysics
Marcel Dekker. M. Watanabe, B. Roux, A. MacKerell, and O. Becker, editors
(2001) , 275-312
PMID: 0     PMCID:

15. Barrientos LG, Campos-Olivas R, Louis JM, Fiser A, Sali A, Gronenborn AM article icon
1H, 13C, 15N resonance assignments and fold verification of a circular permuted variant of the potent HIV-inactivating protein cyanovirin-N.
J Biomol NMR
(2001) 19(3) : 289-90
PMID: 11330821     PMCID:

14. Simon I, Fiser A, Tusnady GE article icon
Predicting protein conformation by statistical methods.
Biochim Biophys Acta
(2001) 1549(2) : 123-36
PMID: 11690649     PMCID:

13. Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Fiser A, Pazos F, Valencia A, Sali A, Rost B article icon
EVA: continuous automatic evaluation of protein structure prediction servers.
(2001) 17(12) : 1242-3
PMID: 11751240     PMCID:

12. Fiser A, Simon I article icon
Predicting the oxidation state of cysteines by multiple sequence alignment.
(2000) 16(3) : 251-6
PMID: 10869018     PMCID:

11. Wu G, McArthur AG, Fiser A, Sali A, Sogin ML, Mllerm M article icon
Core histones of the amitochondriate protist, Giardia lamblia.
Mol Biol Evol
(2000) 17(8) : 1156-63
PMID: 10908635     PMCID:

10. Fiser A, Do RK, Sali A article icon
Modeling of loops in protein structures.
Protein Sci
(2000) 9(9) : 1753-73
PMID: 11045621     PMCID: PMC2144714

9. Fiser A, Vertessy BG article icon
Altered subunit communication in subfamilies of trimeric dUTPases.
Biochem Biophys Res Commun
(2000) 279(2) : 534-42
PMID: 11118321     PMCID:

8. Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A article icon
Comparative protein structure modeling of genes and genomes.
Annu Rev Biophys Biomol Struct
(2000) 29, 291-325
PMID: 10940251     PMCID:

7. Wu G, Fiser A, ter Kuile B, Sali A, Muller M article icon
Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase.
Proc Natl Acad Sci U S A
(1999) 96(11) : 6285-90
PMID: 10339579     PMCID: PMC26873

6. Fiser A, Dosztanyi Z, Simon I article icon
The role of long-range interactions in defining the secondary structure of proteins is overestimated.
Comput Appl Biosci
(1997) 13(3) : 297-301
PMID: 9183535     PMCID:

5. Dosztanyi Z, Fiser A, Simon I article icon
Stabilization centers in proteins: identification, characterization and predictions.
J Mol Biol
(1997) 272(4) : 597-612
PMID: 9325115     PMCID:

4. Fiser A, Simon I, Barton GJ article icon
Conservation of amino acids in multiple alignments: aspartic acid has unexpected conservation.
(1996) 397(2-3) : 225-9
PMID: 8955352     PMCID:

3. Tudos E, Fiser A, Simon I article icon
Different sequence environments of amino acid residues involved and not involved in long-range interactions in proteins.
Int J Pept Protein Res
(1994) 43(2) : 205-8
PMID: 8200741     PMCID:

2. Fiser A, Tusnady GE, Simon I article icon
Chaos game representation of protein structures.
J Mol Graph
(1994) 12(4) : 302-4, 295
PMID: 7696222     PMCID:

1. Fiser A, Cserzo M, Tudos E, Simon I article icon
Different sequence environments of cysteines and half cystines in proteins. Application to predict disulfide forming residues.
(1992) 302(2) : 117-20
PMID: 1633841     PMCID: